data_4PJ8 # _model_server_result.job_id 6ji3O6KvjDVT6ItBga1l9w _model_server_result.datetime_utc '2024-11-07 23:39:39' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4pj8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 4PJ8 # _exptl.entry_id 4PJ8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 316.31 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 4PJ8 _cell.length_a 113.57 _cell.length_b 113.57 _cell.length_c 227.981 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PJ8 _symmetry.cell_setting . _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 99 A CYS 98 1_555 A SG CYS 162 A CYS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 201 A CYS 200 1_555 A SG CYS 257 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 C SG CYS 22 C CYS 22 1_555 C SG CYS 88 C CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf5 C SG CYS 132 C CYS 132 1_555 C SG CYS 182 C CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf6 C SG CYS 157 C CYS 157 1_555 D SG CYS 174 D CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf7 D SG CYS 24 D CYS 23 1_555 D SG CYS 95 D CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 D SG CYS 148 D CYS 147 1_555 D SG CYS 213 D CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A NZ LYS 44 A LYS 43 1_555 E C7 2LJ . A 2LJ 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? metalc ? metalc1 C OG1 THR 26 C THR 26 1_555 F NA NA . C NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.024 ? metalc ? metalc2 C OG SER 27 C SER 27 1_555 F NA NA . C NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc3 C OG SER 93 C SER 93 1_555 F NA NA . C NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? # _chem_comp.formula 'C12 H20 N4 O6' _chem_comp.formula_weight 316.31 _chem_comp.id 2LJ _chem_comp.mon_nstd_flag . _chem_comp.name 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O5' C5' 2LJ sing 1 n n C5' C4' 2LJ sing 2 n n O4' C4' 2LJ sing 3 n n C4' C3' 2LJ sing 4 n n O2' C2' 2LJ sing 5 n n C3' C2' 2LJ sing 6 n n C3' O3' 2LJ sing 7 n n C2' C1' 2LJ sing 8 n n C1' N8 2LJ sing 9 n n N8 C8A 2LJ sing 10 n n C8A N1 2LJ sing 11 n n C8A C4A 2LJ doub 12 n n N1 C2 2LJ sing 13 n n N5 C4A 2LJ sing 14 n n N5 C6 2LJ doub 15 n n C4A C4 2LJ sing 16 n n C8 C7 2LJ sing 17 n n C2 O2 2LJ doub 18 n n C2 N3 2LJ sing 19 n n C7 C6 2LJ sing 20 n n N3 C4 2LJ sing 21 n n C4 O4 2LJ doub 22 n n C6 H1 2LJ sing 23 n n C7 H2 2LJ sing 24 n n C7 H3 2LJ sing 25 n n C8 H4 2LJ sing 26 n n C8 H5 2LJ sing 27 n n C8 H6 2LJ sing 28 n n N3 H7 2LJ sing 29 n n N8 H9 2LJ sing 30 n n C1' H10 2LJ sing 31 n n C1' H11 2LJ sing 32 n n C2' H12 2LJ sing 33 n n O2' H13 2LJ sing 34 n n C3' H14 2LJ sing 35 n n O3' H15 2LJ sing 36 n n C4' H16 2LJ sing 37 n n O4' H17 2LJ sing 38 n n C5' H18 2LJ sing 39 n n C5' H19 2LJ sing 40 n n O5' H20 2LJ sing 41 n n N1 H8 2LJ sing 42 n n # _atom_sites.entry_id 4PJ8 _atom_sites.fract_transf_matrix[1][1] 0.008805 _atom_sites.fract_transf_matrix[1][2] 0.005084 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010167 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004386 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code E 5 2LJ A 1 301 1 2LJ DRG . F 6 NA C 1 301 1 NA NA . G 7 HOH A 1 401 6 HOH HOH . G 7 HOH A 2 402 12 HOH HOH . H 7 HOH B 1 101 24 HOH HOH . I 7 HOH C 1 401 34 HOH HOH . I 7 HOH C 2 402 17 HOH HOH . I 7 HOH C 3 403 73 HOH HOH . J 7 HOH D 1 301 94 HOH HOH . J 7 HOH D 2 302 41 HOH HOH . J 7 HOH D 3 303 98 HOH HOH . J 7 HOH D 4 304 138 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C4 2LJ . . . E 5 -1.221 -38.036 -19.521 1 50.25 ? C4 2LJ 301 A 1 HETATM 2 C C6 2LJ . . . E 5 -1.321 -36.902 -22.327 1 51.06 ? C6 2LJ 301 A 1 HETATM 3 C C7 2LJ . . . E 5 -1.307 -36.313 -23.755 1 53.79 ? C7 2LJ 301 A 1 HETATM 4 C C8 2LJ . . . E 5 -2.227 -36.897 -24.79 1 54.34 ? C8 2LJ 301 A 1 HETATM 5 N N1 2LJ . . . E 5 -3.196 -40.016 -19.25 1 52.66 ? N1 2LJ 301 A 1 HETATM 6 N N3 2LJ . . . E 5 -1.384 -38.833 -18.398 1 51.34 ? N3 2LJ 301 A 1 HETATM 7 N N5 2LJ . . . E 5 -2.212 -37.735 -21.871 1 49.33 ? N5 2LJ 301 A 1 HETATM 8 C C4A 2LJ . . . E 5 -2.209 -38.303 -20.597 1 50.61 ? C4A 2LJ 301 A 1 HETATM 9 O O4 2LJ . . . E 5 -0.264 -37.269 -19.586 1 49.79 ? O4 2LJ 301 A 1 HETATM 10 C C2 2LJ . . . E 5 -2.31 -39.833 -18.221 1 53.21 ? C2 2LJ 301 A 1 HETATM 11 O O2 2LJ . . . E 5 -2.271 -40.599 -17.255 1 54.89 ? O2 2LJ 301 A 1 HETATM 12 C C8A 2LJ . . . E 5 -3.188 -39.313 -20.417 1 52.79 ? C8A 2LJ 301 A 1 HETATM 13 N N8 2LJ . . . E 5 -4.028 -39.714 -21.433 1 54.89 ? N8 2LJ 301 A 1 HETATM 14 C C1' 2LJ . . . E 5 -4.855 -40.907 -21.356 1 57.07 ? C1' 2LJ 301 A 1 HETATM 15 C C2' 2LJ . . . E 5 -6.328 -40.577 -20.976 1 60.39 ? C2' 2LJ 301 A 1 HETATM 16 O O2' 2LJ . . . E 5 -6.779 -39.429 -21.702 1 62.55 ? O2' 2LJ 301 A 1 HETATM 17 C C3' 2LJ . . . E 5 -6.519 -40.409 -19.467 1 58.84 ? C3' 2LJ 301 A 1 HETATM 18 O O3' 2LJ . . . E 5 -5.738 -41.359 -18.751 1 56.34 ? O3' 2LJ 301 A 1 HETATM 19 C C4' 2LJ . . . E 5 -7.963 -40.521 -18.98 1 59.89 ? C4' 2LJ 301 A 1 HETATM 20 O O4' 2LJ . . . E 5 -7.959 -40.137 -17.607 1 60.47 ? O4' 2LJ 301 A 1 HETATM 21 C C5' 2LJ . . . E 5 -8.508 -41.937 -19.082 1 61.56 ? C5' 2LJ 301 A 1 HETATM 22 O O5' 2LJ . . . E 5 -9.723 -42.083 -18.368 1 62.81 ? O5' 2LJ 301 A 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 22 #